AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene053817

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene053817.t1 MTR_5g056450 93.671 158 10 0 1 158 1 158 3.88e-99 282
MS.gene053817.t1 MTR_1g041455 57.471 174 51 5 1 158 1 167 4.00e-57 176
MS.gene053817.t1 MTR_1g048880 46.784 171 60 7 1 158 1 153 2.02e-31 110
MS.gene053817.t1 MTR_1g075780 35.032 157 78 6 11 158 4 145 2.96e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATTGATTTCATTGATT+TGG 0.224195 5.1:+44330136 MS.gene053817:CDS
CATTTGAAGATTCTCCTTCT+AGG 0.234818 5.1:-44330070 None:intergenic
GGCCGAATCACCGTTGGTTT+TGG 0.304502 5.1:-44329966 None:intergenic
AAATCCAATGGATTAACATC+TGG 0.363954 5.1:-44330179 None:intergenic
CTCCTTCTAGGTGCTTTGAT+TGG 0.380419 5.1:-44330058 None:intergenic
TGCTTTGATTGGCAAGCATT+TGG 0.393167 5.1:-44330047 None:intergenic
AACCAAAACCAACGGTGATT+CGG 0.418396 5.1:+44329964 MS.gene053817:CDS
CTGGTGAGTTTAGTAATATT+AGG 0.423811 5.1:+44329745 MS.gene053817:CDS
TGAATAAAGCTTTCTGATTG+TGG 0.433760 5.1:-44329871 None:intergenic
TGCCAATCAAAGCACCTAGA+AGG 0.436715 5.1:+44330056 MS.gene053817:CDS
GAAGGAGAATCTTCAAATGA+TGG 0.491518 5.1:+44330074 MS.gene053817:CDS
TAACCCAGATGTTAATCCAT+TGG 0.496678 5.1:+44330175 MS.gene053817:CDS
AATCCAATGGATTAACATCT+GGG 0.500492 5.1:-44330178 None:intergenic
ATCTTCAAATGATGGTACTA+AGG 0.506473 5.1:+44330082 MS.gene053817:CDS
GGCTGAGGCCGAATCACCGT+TGG 0.513154 5.1:-44329972 None:intergenic
AAAGGGTTTCTGCTTGGCTG+AGG 0.532206 5.1:-44329987 None:intergenic
CATGATGTGTCAAACTTGGT+AGG 0.541015 5.1:+44329768 MS.gene053817:CDS
TGCAACATCATCACCATGGC+TGG 0.552771 5.1:+44329726 None:intergenic
AATCAGAAAGCTTTATTCAA+CGG 0.559288 5.1:+44329875 MS.gene053817:CDS
TAGGCATGATGTGTCAAACT+TGG 0.564079 5.1:+44329764 MS.gene053817:CDS
AGCTTAAGTGATAAATCCAA+TGG 0.575565 5.1:-44330191 None:intergenic
CAATGTTTGCCACCACATGA+TGG 0.576640 5.1:+44329930 MS.gene053817:CDS
AACTCACATCGAGTCTCACA+TGG 0.586787 5.1:+44329836 MS.gene053817:CDS
TTTGATTGGCAAGCATTTGG+TGG 0.591741 5.1:-44330044 None:intergenic
ATTACTAAACTCACCAGCCA+TGG 0.594645 5.1:-44329739 None:intergenic
TCATGTGGTGGCAAACATTG+AGG 0.597472 5.1:-44329927 None:intergenic
GCATTTGCCGATAACCAACA+TGG 0.630189 5.1:-44330016 None:intergenic
ATGATGTGTCAAACTTGGTA+GGG 0.645237 5.1:+44329769 MS.gene053817:CDS
TGTGGTGGCAAACATTGAGG+AGG 0.673338 5.1:-44329924 None:intergenic
GTCTCACATGGAGTACGAAG+AGG 0.675983 5.1:+44329848 MS.gene053817:CDS
AAAATCTTGCCATCATGTGG+TGG 0.685328 5.1:-44329939 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAATCAATTTTCTTGAT+AGG - chr5.1:44330131-44330150 None:intergenic 20.0%
!!! GAAAATTGATTTCATTGATT+TGG + chr5.1:44330136-44330155 MS.gene053817:CDS 20.0%
!!! AATCAGAAAGCTTTATTCAA+CGG + chr5.1:44329875-44329894 MS.gene053817:CDS 25.0%
AGCTTAAGTGATAAATCCAA+TGG - chr5.1:44330194-44330213 None:intergenic 30.0%
ATCTTCAAATGATGGTACTA+AGG + chr5.1:44330082-44330101 MS.gene053817:CDS 30.0%
CTGGTGAGTTTAGTAATATT+AGG + chr5.1:44329745-44329764 MS.gene053817:CDS 30.0%
TGAATAAAGCTTTCTGATTG+TGG - chr5.1:44329874-44329893 None:intergenic 30.0%
TTTGAGTGTTTGTGAAAAAG+CGG - chr5.1:44329809-44329828 None:intergenic 30.0%
!! AAATCCAATGGATTAACATC+TGG - chr5.1:44330182-44330201 None:intergenic 30.0%
!! AATCCAATGGATTAACATCT+GGG - chr5.1:44330181-44330200 None:intergenic 30.0%
!! GATTTTTCAACCAAAACCAA+CGG + chr5.1:44329956-44329975 MS.gene053817:CDS 30.0%
ATGATGTGTCAAACTTGGTA+GGG + chr5.1:44329769-44329788 MS.gene053817:CDS 35.0%
CATTTGAAGATTCTCCTTCT+AGG - chr5.1:44330073-44330092 None:intergenic 35.0%
GAAGGAGAATCTTCAAATGA+TGG + chr5.1:44330074-44330093 MS.gene053817:CDS 35.0%
TAACCCAGATGTTAATCCAT+TGG + chr5.1:44330175-44330194 MS.gene053817:CDS 35.0%
TGAAAAATCTTGCCATCATG+TGG - chr5.1:44329945-44329964 None:intergenic 35.0%
! GAGGAGGAAATTGTCTTTTA+GGG - chr5.1:44329911-44329930 None:intergenic 35.0%
! TGAGGAGGAAATTGTCTTTT+AGG - chr5.1:44329912-44329931 None:intergenic 35.0%
AAAATCTTGCCATCATGTGG+TGG - chr5.1:44329942-44329961 None:intergenic 40.0%
AACCAAAACCAACGGTGATT+CGG + chr5.1:44329964-44329983 MS.gene053817:CDS 40.0%
AACCAACATGGCCGAAAAAA+GGG - chr5.1:44330007-44330026 None:intergenic 40.0%
CATGATGTGTCAAACTTGGT+AGG + chr5.1:44329768-44329787 MS.gene053817:CDS 40.0%
TAACCAACATGGCCGAAAAA+AGG - chr5.1:44330008-44330027 None:intergenic 40.0%
TAGGCATGATGTGTCAAACT+TGG + chr5.1:44329764-44329783 MS.gene053817:CDS 40.0%
TGCTTTGATTGGCAAGCATT+TGG - chr5.1:44330050-44330069 None:intergenic 40.0%
TTTGATTGGCAAGCATTTGG+TGG - chr5.1:44330047-44330066 None:intergenic 40.0%
!! TTTTCGGCCATGTTGGTTAT+CGG + chr5.1:44330009-44330028 MS.gene053817:CDS 40.0%
!!! CCAAGCAGAAACCCTTTTTT+CGG + chr5.1:44329993-44330012 MS.gene053817:CDS 40.0%
AACTCACATCGAGTCTCACA+TGG + chr5.1:44329836-44329855 MS.gene053817:CDS 45.0%
CAATGTTTGCCACCACATGA+TGG + chr5.1:44329930-44329949 MS.gene053817:CDS 45.0%
CCGAAAAAAGGGTTTCTGCT+TGG - chr5.1:44329996-44330015 None:intergenic 45.0%
CTCCTTCTAGGTGCTTTGAT+TGG - chr5.1:44330061-44330080 None:intergenic 45.0%
GCATTTGCCGATAACCAACA+TGG - chr5.1:44330019-44330038 None:intergenic 45.0%
TCATGTGGTGGCAAACATTG+AGG - chr5.1:44329930-44329949 None:intergenic 45.0%
! TGCCAATCAAAGCACCTAGA+AGG + chr5.1:44330056-44330075 MS.gene053817:CDS 45.0%
!!! AACCCTTTTTTCGGCCATGT+TGG + chr5.1:44330002-44330021 MS.gene053817:CDS 45.0%
AAAGGGTTTCTGCTTGGCTG+AGG - chr5.1:44329990-44330009 None:intergenic 50.0%
GTCTCACATGGAGTACGAAG+AGG + chr5.1:44329848-44329867 MS.gene053817:CDS 50.0%
TGTGGTGGCAAACATTGAGG+AGG - chr5.1:44329927-44329946 None:intergenic 50.0%
!!! GGCCGAATCACCGTTGGTTT+TGG - chr5.1:44329969-44329988 None:intergenic 55.0%
GGCTGAGGCCGAATCACCGT+TGG - chr5.1:44329975-44329994 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 44329741 44330217 44329741 ID=MS.gene053817
chr5.1 mRNA 44329741 44330217 44329741 ID=MS.gene053817.t1;Parent=MS.gene053817
chr5.1 exon 44329741 44330217 44329741 ID=MS.gene053817.t1.exon1;Parent=MS.gene053817.t1
chr5.1 CDS 44329741 44330217 44329741 ID=cds.MS.gene053817.t1;Parent=MS.gene053817.t1
Gene Sequence

>MS.gene053817

ATGGCTGGTGAGTTTAGTAATATTAGGCATGATGTGTCAAACTTGGTAGGGTGTAAATATTGCAACCGCTTTTTCACAAACACTCAAACACTCGTAACTCACATCGAGTCTCACATGGAGTACGAAGAGGCCACAATCAGAAAGCTTTATTCAACGGAGCGTATCAACCCTAAAAGACAATTTCCTCCTCAATGTTTGCCACCACATGATGGCAAGATTTTTCAACCAAAACCAACGGTGATTCGGCCTCAGCCAAGCAGAAACCCTTTTTTCGGCCATGTTGGTTATCGGCAAATGCAACTTCCACCAAATGCTTGCCAATCAAAGCACCTAGAAGGAGAATCTTCAAATGATGGTACTAAGGCATATATCAAGCAACTTGAGAAACCTATCAAGAAAATTGATTTCATTGATTTGGTTAATAATGATGATGATAACCCAGATGTTAATCCATTGGATTTATCACTTAAGCTCTAG
Protein sequence

>MS.gene053817.t1

MAGEFSNIRHDVSNLVGCKYCNRFFTNTQTLVTHIESHMEYEEATIRKLYSTERINPKRQFPPQCLPPHDGKIFQPKPTVIRPQPSRNPFFGHVGYRQMQLPPNACQSKHLEGESSNDGTKAYIKQLEKPIKKIDFIDLVNNDDDNPDVNPLDLSLKL